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Targeted Metagenomics and Ecology of Globally Important Uncultured Eukaryotic Phytoplankton

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Targeted Metagenomics and Ecology of Globally Important Uncultured Eukaryotic Phytoplankton Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton Marie L. Cuveliera,b, Andrew E. Allenc,1, Adam Moniera,1, John P. McCrowc, Monique Messiéa, Susannah G. Tringed, Tanja Woyked, Rory M. Welsha, Thomas Ishoeyc, Jae-Hyeok Leee, Brian J. Binderf, Chris L. DuPontc, Mikel Latasag, Cédric Guigandb, Kurt R. Bucka, Jason Hiltonb, Mathangi Thiagarajanc, Elisabet Calerc, Betsy Readh, Roger S. Laskenc, Francisco P. Chaveza, and Alexandra Z. Wordena,b,2 aMonterey Bay Aquarium Research Institute, Moss Landing, CA 95039; bRosenstiel School of Marine and Atmospheric Science, Miami, FL 33149; cJ. Craig Venter Institute, San Diego, CA 92121; dUS Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; eDepartment of Biology, Washington University, St. Louis, MO 63130; fDepartment of Marine Sciences, University of Georgia, Athens, GA 36072; gInstitut de Ciències del Mar (CSIC), E-08003 Barcelona, Spain; and hDepartment of Biological Sciences, California State University, San Marcos, CA 92096 Edited by David Karl, University of Hawaii, Honolulu, HI, and approved June 21, 2010 (received for review February 18, 2010) Among eukaryotes, four major phytoplankton lineages are respon- Oceanic prymnesiophytes are thought to be small owing to high sible for marine photosynthesis; prymnesiophytes, alveolates, stra- levels of prymnesiophyte-indicative pigments in regions where menopiles, and prasinophytes. Contributions by individual taxa, most Chl a (representing all phytoplankton combined) is in the however, are not well known, and genomes have been analyzed <2-μm size fraction (6, 12). Six picoplanktonic prymnesiophytes from only the latter two lineages. Tiny “picoplanktonic” members of exist in culture (6, 7) but prymnesiophyte 18S rDNA sequences the prymnesiophyte lineage have long been inferred to be ecolog- from <2–3-μm size-fractioned environmental samples typically ically important but remain poorly characterized. Here, we examine belong to uncultured taxa (6, 13–15). As a whole, this lineage pico-prymnesiophyte evolutionary history and ecology using culti- reportedly diverged from other major eukaryotic lineages early vation-independent methods. 18S rRNA gene analysis showed pico- on, 1.2 billion years ago (16), and their overall placement among prymnesiophytes belonged to broadly distributed uncultivated eukaryotes is uncertain (4, 16). They are extremely distant from taxa. Therefore, we used targeted metagenomics to analyze uncul- phytoplankton with published genomes. Thus, although infer- tured pico-prymnesiophytes sorted by flow cytometry from sub- ences exist regarding their importance and evolutionary history, tropical North Atlantic waters. The data reveal a composite uncertainties surround even the most basic features of oceanic nuclear-encoded gene repertoire with strong green-lineage affilia- pico-prymnesiophytes, such as cell size, biomass, growth rates, and tions, which contrasts with the evolutionary history indicated by the genomic composition. plastid genome. Measured pico-prymnesiophyte growth rates were One approach for gaining insights to uncultivated taxa is meta- rapid in this region, resulting in primary production contributions genomics. However, unicellular eukaryotes have larger genomes Prochlorococcus and lower gene density than marine bacteria and archaea and are similar to the cyanobacterium . On average, pico- fi fi prymnesiophytes formed 25% of global picophytoplankton bio- less abundant, making ef cient sequence recovery dif cult by seawater filtration. Parsing of eukaryotic data from diverse com- mass, with differing contributions in five biogeographical provinces munities is particularly problematic owing to the paucity of relevant spanning tropical to subpolar systems. Elements likely contributing reference genomes. Selection of DNA from an uncultivated target to success include high gene density and genes potentially involved microbe(s) (e.g., by fosmid sequencing or using cells sorted by flow in defense and nutrient uptake. Our findings have implications cytometry) obviates bioinformatic parsing issues and has revealed reaching beyond pico-prymnesiophytes, to the prasinophytes and unique gene complements in uncultured prokaryotes (17, 18). stramenopiles. For example, prevalence of putative Ni-containing To address uncertainties regarding pico-prymnesiophyte ecol- superoxide dismutases (SODs), instead of Fe-containing SODs, ogy, we integrated a suite of cultivation-independent methods. seems to be a common adaptation among eukaryotic phytoplank- Targeted metagenomics was developed to investigate diversity ton for reducing Fe quotas in low-Fe modern oceans. Moreover, and genomic features of uncultivated pico-prymnesiophytes. highly mosaic gene repertoires, although compositionally distinct Growth rates were measured and used to assess primary pro- for each major eukaryotic lineage, now seem to be an underlying duction in the same region. Building on this contextual dataset, facet of successful marine phytoplankton. biomass contributions were evaluated across provinces spanning tropical to subpolar systems, providing a comprehensive view of comparative genomics | primary production | prymnesiophytes | marine global importance and latitudinal variations. photosynthesis | haptophytes lobal primary production is partitioned equally among terres- Author contributions: M.L.C., T.I., R.S.L., and A.Z.W. designed research; M.L.C., A.M., Gtrial and marine ecosystems, each accounting for ≈50 gigatons S.G.T., T.W., R.M.W., T.I., B.J.B., M.L., C.G., K.R.B., J.H., and A.Z.W. performed research; B.R. of carbon per year (1). The phytoplankton responsible for marine contributed new reagents/analytic tools; M.L.C., A.E.A., A.M., J.P.M., M.M., S.G.T., T.W., J.-H.L., C.L.D., M.L., M.T., E.C., F.P.C., and A.Z.W. analyzed data; and M.L.C., A.E.A., J.P.M., primary production include the cyanobacteria, Prochlorococcus and S.G.T., T.W., and A.Z.W. wrote the paper. Synechococcus, and a multitude of eukaryotic phytoplankton, such as The authors declare no conflict of interest. diatoms, dinoflagellates, prasinophytes, and prymnesiophytes (2–4). “ ” < – μ Data deposition: The sequences reported in this paper have been deposited in the Gen- Most oceanic phytoplankton are picoplanktonic ( 2 3 mdi- Bank database (accession nos. HM581528–HM581638 and HM565909–HM565914). Other ameter) and have high surface area to volume ratios, an advantage in scaffolds with predicted genes from this Whole Genome Shotgun/454 project have been open-ocean low-nutrient conditions (5–8). Despite the importance deposited at DNA Data Bank of Japan/European Molecular Biology Laboratory/GenBank of eukaryotic phytoplankton to carbon cycling only six genomes have under the accession no. AEAR00000000. The version described in this paper is the first been sequenced and analyzed comparatively, all being from diatoms version, AEAR01000000. and prasinophytes. These revealed greater differentiation than an- This article is a PNAS Direct Submission. ticipated on the basis of 18S rRNA gene analyses (9–11). The ob- Freely available online through the PNAS open access option. served genomic divergence is associated with major differences in 1A.E.A. and A.M. contributed equally to this work. 2 physiology and niche adaptation (10). To whom correspondence should be addressed. E-mail: [email protected]. SCIENCES Pigment-based estimates indicate that prymnesiophytes, also This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. ENVIRONMENTAL known as haptophytes, are broadly distributed and abundant. 1073/pnas.1001665107/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1001665107 PNAS | August 17, 2010 | vol. 107 | no. 33 | 14679–14684 Downloaded by guest on October 1, 2021 Results and Discussion and Sanger technologies (SI Materials and Methods, Section 5). Eukaryote-Targeted Metagenomics Approach and Diversity Context. Genes were modeled on assembled scaffolds and then screened Photosynthetic picoeukaryote populations were sorted by flow phylogenetically using the E. huxleyi nuclear genome. For selection, fi cytometry (hereafter “sorted” or “the sort”) based on scatter and half the identi able genes on a scaffold had to clade directly with autofluorescence characteristics from two subtropical North At- E. huxleyi, to the exclusion of gene sequences from all other taxa (SI lantic samples collected in the Florida Straits (Fig. 1, Fig. 2 Inset, Materials and Methods, Section 6). This ensured that only prymne- and SI Materials and Methods, Sections 1 and 2). Whole-genome siophyte-derived scaffolds were further analyzed, because the stra- amplification (19) was performed on sorted target populations (SI menopile Pelagomonas fell partially in the same flow-cytometric Materials and Methods, Section 3), providing unprecedented access population (SI Materials and Methods, Section 5). Seventy-one per- to pico-prymnesiophyte DNA. cent of genes on selected scaffolds were sistered by E. huxleyi genes, The sorted pico-prymnesiophytes were distinct from cultured demonstrating screening rigor; only this scaffold subset (2 MB of taxa but closely related to environmental sequences from native assembly) was considered unambiguously pico-prymnesiophyte populations. 18S rDNA clone libraries built from the sort DNA derived and used for comparative analyses. Twenty-nine percent of were analyzed within the context of <2–3 μm size-fractionated genes on pico-prymnesiophyte scaffolds seemed to be missing from clone libraries from
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